7 Search Results for "Wilson, Walter W."

Document
DOI: 10.4230/LIPIcs.GD.2025.35
A Walk on the Wild Side: A Shape-First Methodology for Orthogonal Drawings

Authors: Giordano Andreola, Susanna Caroppo, Giuseppe Di Battista, Fabrizio Grosso, Maurizio Patrignani, and Allegra Strippoli

Published in: LIPIcs, Volume 357, 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)

Abstract
Several algorithms for the construction of orthogonal drawings of graphs, including those based on the Topology-Shape-Metrics (TSM) paradigm, tend to prioritize the minimization of crossings. This emphasis has two notable side effects: some edges are drawn with unnecessarily long sequences of segments and bends, and the overall drawing area may become excessively large. As a result, the produced drawings often lack geometric uniformity. Moreover, orthogonal crossings are known to have a limited impact on readability, suggesting that crossing minimization may not always be the optimal goal. In this paper, we introduce a methodology that "subverts" the traditional TSM pipeline by focusing on minimizing bends. Given a graph G, we ideally seek to construct a rectilinear drawing of G, that is, an orthogonal drawing with no bends. When not possible, we incrementally subdivide the edges of G by introducing dummy vertices that will (possibly) correspond to bends in the final drawing. This process continues until a rectilinear drawing of a subdivision of the graph is found, after which the final coordinates are computed. We tackle the (NP-complete) rectilinear drawability problem by encoding it as a SAT formula and solving it with state-of-the-art SAT solvers. If the SAT formula is unsatisfiable, we use the solver’s proof to determine which edge to subdivide. Our implementation, domus, which is fairly simple, is evaluated through extensive experiments on small- to medium-sized graphs. The results show that it consistently outperforms ogdf’s TSM-based approach across most standard graph drawing metrics.
Cite as

Giordano Andreola, Susanna Caroppo, Giuseppe Di Battista, Fabrizio Grosso, Maurizio Patrignani, and Allegra Strippoli. A Walk on the Wild Side: A Shape-First Methodology for Orthogonal Drawings. In 33rd International Symposium on Graph Drawing and Network Visualization (GD 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 357, pp. 35:1-35:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{andreola_et_al:LIPIcs.GD.2025.35,
  author =	{Andreola, Giordano and Caroppo, Susanna and Di Battista, Giuseppe and Grosso, Fabrizio and Patrignani, Maurizio and Strippoli, Allegra},
  title =	{{A Walk on the Wild Side: A Shape-First Methodology for Orthogonal Drawings}},
  booktitle =	{33rd International Symposium on Graph Drawing and Network Visualization (GD 2025)},
  pages =	{35:1--35:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-403-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{357},
  editor =	{Dujmovi\'{c}, Vida and Montecchiani, Fabrizio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.GD.2025.35},
  URN =		{urn:nbn:de:0030-drops-250218},
  doi =		{10.4230/LIPIcs.GD.2025.35},
  annote =	{Keywords: Non-planar Orthogonal Drawings, SAT Solver, Experimental Comparison}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.43
Edge Clique Partition and Cover Beyond Independence

Authors: Fedor V. Fomin, Petr A. Golovach, Danil Sagunov, and Kirill Simonov

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
Covering and partitioning the edges of a graph into cliques are classical problems at the intersection of combinatorial optimization and graph theory, having been studied through a range of algorithmic and complexity-theoretic lenses. Despite the well-known fixed-parameter tractability of these problems when parameterized by the total number of cliques, such a parameterization often fails to be meaningful for sparse graphs. In many real-world instances, on the other hand, the minimum number of cliques in an edge cover or partition can be very close to the size of a maximum independent set α(G). Motivated by this observation, we investigate above-α parameterizations of the edge clique cover and partition problems. Concretely, we introduce and study Edge Clique Cover Above Independent Set (ECC/α) and Edge Clique Partition Above Independent Set (ECP/α), where the goal is to cover or partition all edges of a graph using at most α(G) + k cliques, and k is the parameter. Our main results reveal a distinct complexity landscape for the two variants. We show that ECP/α is fixed-parameter tractable, whereas ECC/α is NP-complete for all k ≥ 2, yet can be solved in polynomial time for k ∈ {0,1}. These findings highlight intriguing differences between the two problems when viewed through the lens of parameterization above a natural lower bound. Finally, we demonstrate that ECC/α becomes fixed-parameter tractable when parameterized by k + ω(G), where ω(G) is the size of a maximum clique of the graph G. This result is particularly relevant for sparse graphs, in which ω is typically small. For H-minor free graphs, we design a subexponential algorithm of running time f(H)^√k ⋅ n^𝒪(1).
Cite as

Fedor V. Fomin, Petr A. Golovach, Danil Sagunov, and Kirill Simonov. Edge Clique Partition and Cover Beyond Independence. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 43:1-43:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{fomin_et_al:LIPIcs.ESA.2025.43,
  author =	{Fomin, Fedor V. and Golovach, Petr A. and Sagunov, Danil and Simonov, Kirill},
  title =	{{Edge Clique Partition and Cover Beyond Independence}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{43:1--43:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.43},
  URN =		{urn:nbn:de:0030-drops-245113},
  doi =		{10.4230/LIPIcs.ESA.2025.43},
  annote =	{Keywords: edge clique partition, edge clique cover, independence number, parameterized complexity, above guarantee}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.WABI.2025.5
Improved Algorithms for Bi-Partition Function Computation

Authors: John D. Bridgers, Jan Hoinka, S. Cenk Sahinalp, Salem Malikic, Teresa M. Przytycka, and Funda Ergun

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
The evolutionary history of a tumor, inferred from single-cell sequencing data, is typically represented as a tree in which each subtree corresponds to a clade of cells seeded by a specific set of mutations. Traditional methods typically identify a single most likely tree for downstream analyses, such as detecting driver mutations, studying mutation co-occurrence patterns and identifying common evolutionary trajectories. However, the reliability of such inferred trees, particularly their topology, clade composition, and mutational placements, often remains uncertain. To quantify this uncertainty, the concept of a Bi-partition Function was recently introduced, providing a probabilistic measure of how reliably a mutation seeds a given clade of cells. The single available algorithm for estimating the Bi-partition Function relies on simplifying assumptions and uses sampling for limited exploration of the tree-space. In this paper, we introduce the first exact algorithm for computing the Bi-partition Function. Our algorithm scales linearly with the number of mutations but exhibits super-exponential complexity with respect to the number of cells. Despite this complexity, it establishes crucial ground truth values, essential for accurately benchmarking and validating approximate methods. Additionally, we present a GPU-accelerated version of the available sampling-based algorithm, significantly boosting the computational performance through large-scale parallelization, enabling more accurate Bi-partition Function estimates via deeper exploration of the tree spaces. We compare our methods on synthetic datasets, demonstrating that especially when the number of mutations sufficiently exceed the number of cells, our GPU-accelerated sampling algorithm closely approximates the exact ground truth values.
Cite as

John D. Bridgers, Jan Hoinka, S. Cenk Sahinalp, Salem Malikic, Teresa M. Przytycka, and Funda Ergun. Improved Algorithms for Bi-Partition Function Computation. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 5:1-5:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bridgers_et_al:LIPIcs.WABI.2025.5,
  author =	{Bridgers, John D. and Hoinka, Jan and Sahinalp, S. Cenk and Malikic, Salem and Przytycka, Teresa M. and Ergun, Funda},
  title =	{{Improved Algorithms for Bi-Partition Function Computation}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{5:1--5:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.5},
  URN =		{urn:nbn:de:0030-drops-239318},
  doi =		{10.4230/LIPIcs.WABI.2025.5},
  annote =	{Keywords: Tumor Evolution, Bi-partition Function, Single-Cell Sequencing, Algorithms}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.8
Rapid Mixing of the Flip Chain over Non-Crossing Spanning Trees

Authors: Konrad Anand, Weiming Feng, Graham Freifeld, Heng Guo, Mark Jerrum, and Jiaheng Wang

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
We show that the flip chain for non-crossing spanning trees of n+1 points in convex position mixes in time O(n⁸log n). We use connections between Fuss-Catalan structures to construct a comparison argument with a chain similar to Wilson’s lattice path chain (Wilson 2004).
Cite as

Konrad Anand, Weiming Feng, Graham Freifeld, Heng Guo, Mark Jerrum, and Jiaheng Wang. Rapid Mixing of the Flip Chain over Non-Crossing Spanning Trees. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 8:1-8:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{anand_et_al:LIPIcs.SoCG.2025.8,
  author =	{Anand, Konrad and Feng, Weiming and Freifeld, Graham and Guo, Heng and Jerrum, Mark and Wang, Jiaheng},
  title =	{{Rapid Mixing of the Flip Chain over Non-Crossing Spanning Trees}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{8:1--8:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.8},
  URN =		{urn:nbn:de:0030-drops-231607},
  doi =		{10.4230/LIPIcs.SoCG.2025.8},
  annote =	{Keywords: non-crossing spanning trees, Markov chain, mixing time}
}
Document
Vision
DOI: 10.4230/TGDK.1.1.3
Knowledge Engineering Using Large Language Models

Authors: Bradley P. Allen, Lise Stork, and Paul Groth

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
Knowledge engineering is a discipline that focuses on the creation and maintenance of processes that generate and apply knowledge. Traditionally, knowledge engineering approaches have focused on knowledge expressed in formal languages. The emergence of large language models and their capabilities to effectively work with natural language, in its broadest sense, raises questions about the foundations and practice of knowledge engineering. Here, we outline the potential role of LLMs in knowledge engineering, identifying two central directions: 1) creating hybrid neuro-symbolic knowledge systems; and 2) enabling knowledge engineering in natural language. Additionally, we formulate key open research questions to tackle these directions.
Cite as

Bradley P. Allen, Lise Stork, and Paul Groth. Knowledge Engineering Using Large Language Models. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{allen_et_al:TGDK.1.1.3,
  author =	{Allen, Bradley P. and Stork, Lise and Groth, Paul},
  title =	{{Knowledge Engineering Using Large Language Models}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:19},
  ISSN =	{2942-7517},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.3},
  URN =		{urn:nbn:de:0030-drops-194777},
  doi =		{10.4230/TGDK.1.1.3},
  annote =	{Keywords: knowledge engineering, large language models}
}
Document
DOI: 10.4230/LIPIcs.ICLP.2011.290
Implementation of Axiomatic Language

Authors: Walter W. Wilson

Published in: LIPIcs, Volume 11, Technical Communications of the 27th International Conference on Logic Programming (ICLP'11) (2011)

Abstract
This report summarizes a PhD research effort to implement a type of logic programming language called "axiomatic language". Axiomatic language is intended as a specification language, so its implementation involves the transformation of specifications to efficient algorithms. The language is described and the implementation task is discussed.
Cite as

Walter W. Wilson. Implementation of Axiomatic Language. In Technical Communications of the 27th International Conference on Logic Programming (ICLP'11). Leibniz International Proceedings in Informatics (LIPIcs), Volume 11, pp. 290-295, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{wilson:LIPIcs.ICLP.2011.290,
  author =	{Wilson, Walter W.},
  title =	{{Implementation of Axiomatic Language}},
  booktitle =	{Technical Communications of the 27th International Conference on Logic Programming (ICLP'11)},
  pages =	{290--295},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-31-6},
  ISSN =	{1868-8969},
  year =	{2011},
  volume =	{11},
  editor =	{Gallagher, John P. and Gelfond, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICLP.2011.290},
  URN =		{urn:nbn:de:0030-drops-31893},
  doi =		{10.4230/LIPIcs.ICLP.2011.290},
  annote =	{Keywords: axiomatic language, specification, program transformation, unfold/fold}
}
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